The mitochondrial genome as an evolutionary storyteller: a journey from dire wolf (Aenocyon dirus) to extant species of Canini (Carnivora: Canidae)

The dire wolf ( Aenocyon dirus ) was a large canid that roamed the Americas in the Late Pleistocene. The genome of A. dirus was only recently sequenced. This was a turning point in the studies on A. dirus , especially because it refuted the previous hypothesis of a close phylogenetic relationship between dire wolves and grey wolves, placing A. dirus as the sister group of the other canids. Despite this, population studies, usually based on mitochondrial genomes, were absent, and a proper description and annotation of the A. dirus mitochondrial genome are lacking. In our study, we aimed to address this issue. Using previously sequenced DNA from A. dirus , we de novo assembled the complete mitochondrial genome. We also assembled the mitochondrial genomes of several Canini species, many of which are the first descriptions so far, and conducted a phylogenetic analysis. We observed a population-level structure between the eastern and western USA samples of A. dirus . Our comparative analysis further reinforced the mitonuclear discordance by comparing our results with many mitochondrial and nuclear phylogenetic studies. This indicates a complex evolutionary history within different species, with a possible mitochondrial genome capture event happening within the group. Consequently, our work improved the current mitochondrial genome knowledge of the Canini tribe. Our findings will be valuable for future population genetics studies on A. dirus . They also conveyed insights into the mitonuclear discordance across Canini, which can help clarify introgression and mitochondrial genome capture events within the tribe.